I am posting this for an acquaintance who mentioned the problem to me.
He needs to make an RNA probe from a cDNA template by run-off transcription
in vitro. The RNA made incorporates UTP (then he tried CTP) at a very low
efficiency of 1% while the DNA template of the Maxi Script kit produces RNA
with a 50% incorporation. He suspects "rearrangement of some sequences in
the cDNA template during the subcloning which causes early termination of
transcription."
What do you think? Thank you.